OK the issue of copying BRU can be solved by adding the line "copy BRU SYS:Tools CLONE" just under "cd DF0:Tools" in the Extras3.1 script. That line can be commented or removed from the Install3.1 script if you don't want it to throw an error but it's not necessary.

Guys sorry to dig up an old thread but the 3.1x disks, are these the same disks that are on Amiga Forever 7 or are they new ones only available from Cloanto? Asking as I've just dug my A1200 out the loft and was thinking of upgrading the KS and have read that it will need workbench.library on the disk. All 3.1 disks I've seen don't have this.